Variant report

Variant	rs571121877
Chromosome Location	chr2:20425579-20425580
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr2:20424249-20425583	A549	lung:	n/a	chr2:20424895-20424909 chr2:20424470-20424482 chr2:20425525-20425534 chr2:20424990-20424999 chr2:20424936-20424946 chr2:20424951-20424961 chr2:20424950-20424962 chr2:20424471-20424485 chr2:20424991-20425000 chr2:20424950-20424962 chr2:20424896-20424905 chr2:20424989-20425001 chr2:20425525-20425535 chr2:20424951-20424960 chr2:20425524-20425536 chr2:20424951-20424960 chr2:20425524-20425536 chr2:20424990-20425000 chr2:20424951-20424965 chr2:20424472-20424481 chr2:20424895-20424905 chr2:20424989-20425001 chr2:20424990-20425000 chr2:20424952-20424961 chr2:20424951-20424961
2	SIN3A	chr2:20422973-20425643	H1-hESC	embryonic stem cell:	n/a	chr2:20425301-20425312 chr2:20424997-20425010 chr2:20424672-20424683 chr2:20424735-20424748 chr2:20424645-20424656
3	RAD21	chr2:20420269-20426598	SK-N-SH	brain:	n/a	chr2:20422198-20422210 chr2:20424162-20424172 chr2:20425226-20425238 chr2:20423347-20423361
4	EGR1	chr2:20425428-20425631	K562	blood:	n/a	chr2:20425523-20425532 chr2:20425520-20425533
5	NFIC	chr2:20424972-20426031	HepG2	liver:	n/a	n/a
6	EGR1	chr2:20424669-20425725	MCF-7	breast:	n/a	chr2:20424997-20425007 chr2:20424952-20424962 chr2:20424953-20424966 chr2:20425523-20425532 chr2:20424992-20425005 chr2:20425304-20425314 chr2:20425520-20425533
7	POLR2A	chr2:20424370-20425723	MCF-7	breast:	n/a	n/a
8	POLR2A	chr2:20424950-20425955	HepG2	liver:	n/a	n/a
9	MAX	chr2:20425509-20425603	K562	blood:	n/a	n/a
10	ESRRA	chr2:20424274-20426108	GM12878	blood:	n/a	chr2:20425299-20425312 chr2:20425885-20425901
11	ZNF263	chr2:20424394-20426249	HEK293-T-REx	kidney:	n/a	n/a
12	HNF4G	chr2:20425019-20425976	HepG2	liver:	n/a	chr2:20425615-20425627 chr2:20425808-20425822 chr2:20425809-20425822
13	RAD21	chr2:20424977-20425759	MCF-7	breast:	n/a	chr2:20425226-20425238
14	TAF1	chr2:20424959-20425806	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr2:20422503-20426249	HepG2	liver:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
16	POLR2A	chr2:20422936-20425902	MCF-7	breast:	n/a	n/a
17	RAD21	chr2:20424784-20425815	HCT-116	colon:	n/a	chr2:20425226-20425238
18	ZNF143	chr2:20425130-20425846	H1-hESC	embryonic stem cell:	n/a	n/a
19	NR2F2	chr2:20424957-20426048	MCF-7	breast:	n/a	n/a
20	YY1	chr2:20425564-20426061	HepG2	liver:	n/a	chr2:20425836-20425844 chr2:20425825-20425847
21	GTF2F1	chr2:20425270-20425831	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr2:20425440-20425590	HRPEpiC	eye:	n/a	n/a
23	CTCF	chr2:20425520-20425670	HFF-Myc	foreskin:	n/a	n/a
24	CTCF	chr2:20425440-20425590	Caco-2	colon:	n/a	n/a
25	HDAC2	chr2:20422965-20425963	HepG2	liver:	n/a	n/a
26	MYBL2	chr2:20424962-20425949	HepG2	liver:	n/a	n/a
27	MAX	chr2:20424253-20425899	MCF-7	breast:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
28	MAX	chr2:20423554-20425885	ECC-1	luminal epithelium:	n/a	chr2:20424483-20424490 chr2:20424338-20424348 chr2:20424526-20424536
29	RAD21	chr2:20425007-20425711	GM12878	blood:	n/a	chr2:20425226-20425238
30	YY1	chr2:20425465-20426067	H1-hESC	embryonic stem cell:	n/a	chr2:20425836-20425844 chr2:20425825-20425847
31	BACH1	chr2:20425034-20425769	H1-hESC	embryonic stem cell:	n/a	n/a
32	ZBTB7A	chr2:20422937-20425652	ECC-1	luminal epithelium:	n/a	chr2:20423177-20423184 chr2:20425227-20425236 chr2:20423506-20423515
33	RAD21	chr2:20424981-20425639	MCF-7	breast:	n/a	chr2:20425226-20425238
34	CTCF	chr2:20425480-20425630	Caco-2	colon:	n/a	n/a
35	TBP	chr2:20424795-20425858	H1-hESC	embryonic stem cell:	n/a	n/a
36	HEY1	chr2:20425563-20425973	HepG2	liver:	n/a	n/a
37	FOSL2	chr2:20424964-20425579	A549	lung:	n/a	chr2:20425195-20425204
38	POLR2A	chr2:20424943-20425987	H1-hESC	embryonic stem cell:	n/a	n/a
39	MYBL2	chr2:20424431-20426143	HepG2	liver:	n/a	n/a
40	MAX	chr2:20424824-20425715	MCF-7	breast:	n/a	n/a
41	MAX	chr2:20422708-20425903	A549	lung:	n/a	chr2:20423191-20423198 chr2:20424483-20424490 chr2:20423189-20423200 chr2:20424338-20424348 chr2:20423190-20423199 chr2:20423540-20423550 chr2:20423190-20423200 chr2:20424526-20424536 chr2:20423189-20423199
42	POLR2A	chr2:20424977-20425807	H1-hESC	embryonic stem cell:	n/a	n/a
43	RAD21	chr2:20424833-20425677	HCT-116	colon:	n/a	chr2:20425226-20425238
44	MTA3	chr2:20424906-20425655	GM12878	blood:	n/a	n/a
45	RAD21	chr2:20424652-20425634	SK-N-SH_RA	brain:	n/a	chr2:20425226-20425238
46	POLR2A	chr2:20422475-20425920	HepG2	liver:	n/a	n/a
47	HNF4A	chr2:20425072-20426030	HepG2	liver:	n/a	chr2:20425988-20425996 chr2:20425615-20425627 chr2:20425808-20425822 chr2:20425809-20425822
48	MAX	chr2:20424979-20426145	H1-hESC	embryonic stem cell:	n/a	n/a
49	E2F6	chr2:20424981-20426097	H1-hESC	embryonic stem cell:	n/a	chr2:20425402-20425411
50	YY1	chr2:20424959-20425599	A549	lung:	n/a	chr2:20425301-20425312

No.	Distal block	Cell Line	Cell type
1	chr2:20299695..20307724-chr2:20421846..20426859,15	MCF-7	breast:
2	chr2:20306351..20307044-chr2:20424834..20425592,2	MCF-7	breast:
3	chr2:20424066..20426931-chr2:20646792..20649592,2	MCF-7	breast:
4	chr2:20422608..20425941-chr2:20442995..20447318,5	MCF-7	breast:
5	chr2:20249233..20252415-chr2:20424056..20425890,4	MCF-7	breast:
6	chr2:20097107..20100415-chr2:20424161..20425989,3	K562	blood:
7	chr2:20421499..20423791-chr2:20425335..20427623,2	K562	blood:

Variant related genes	Relation type
SDC1	TF binding region
ENSG00000234378	Chromatin interaction
ENSG00000223734	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000238735	Chromatin interaction
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846803	chr2:20409322-20427189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	esv3429530	chr2:20423096-20425644	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	esv1798036	chr2:20423264-20442631	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1846193	chr2:20423264-20442631	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv1849406	chr2:20423264-20442631	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1819683	chr2:20423264-20455467	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3398925	chr2:20423871-20426119	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20422600-20425600	Active TSS	Fetal Brain Female	brain
2	chr2:20422600-20425800	Active TSS	Rectal Smooth Muscle	rectum
3	chr2:20422800-20425600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:20422800-20425600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:20422800-20425600	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr2:20422800-20426000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:20423000-20425600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:20423000-20425600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr2:20423000-20425600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr2:20423000-20425600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:20423000-20425600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:20423000-20425600	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr2:20423000-20425600	Active TSS	Colon Smooth Muscle	Colon
14	chr2:20423000-20425600	Active TSS	Hela-S3	cervix
15	chr2:20423000-20425800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr2:20423000-20425800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:20423000-20425800	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr2:20423000-20425800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:20423200-20425600	Active TSS	H1 Cell Line	embryonic stem cell
20	chr2:20423200-20425600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr2:20423200-20425600	Active TSS	HSMMtube	muscle
22	chr2:20423400-20425800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
23	chr2:20423600-20425600	Active TSS	Psoas Muscle	Psoas
24	chr2:20423600-20425600	Active TSS	K562	blood
25	chr2:20423800-20425600	Active TSS	NHEK	skin
26	chr2:20423800-20425600	Active TSS	NHLF	lung
27	chr2:20424000-20425600	Active TSS	Brain Germinal Matrix	brain
28	chr2:20424200-20425600	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr2:20424200-20425800	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr2:20424400-20425600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr2:20424600-20425600	Active TSS	Muscle Satellite Cultured Cells	--
32	chr2:20424600-20425600	Active TSS	Fetal Kidney	kidney
33	chr2:20425000-20425600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
34	chr2:20425000-20425600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:20425000-20425600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:20425000-20425600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
37	chr2:20425000-20425600	Flanking Active TSS	HUVEC	blood vessel
38	chr2:20425000-20425800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr2:20425000-20425800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
40	chr2:20425000-20425800	Enhancers	Fetal Brain Male	brain
41	chr2:20425000-20425800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr2:20425200-20425600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:20425200-20425600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
44	chr2:20425200-20425600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:20425200-20425600	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr2:20425200-20425600	Flanking Active TSS	Placenta	Placenta
47	chr2:20425200-20425600	Flanking Active TSS	Placenta Amnion	Placenta Amnion
48	chr2:20425200-20425600	Flanking Active TSS	Right Ventricle	heart
49	chr2:20425200-20425600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
50	chr2:20425200-20425600	Flanking Active TSS	Stomach Mucosa	stomach

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